Activity for Yannick Djoumbou

  • Yannick Djoumbou Yannick Djoumbou posted a comment on ticket #112

    Hi Nina, I guess I was tired of trying :). Here is the pom.xml with the correct spelling. Same error message. However, I noticed that I need to specify the repositories, and after tryig a few times, I follwed the convention below, and it worked. 1) To import a release (e.g.: 3.2.0), I added the following: <repositories> <repository> <id>nexus-idea-releases</id> <url>https://nexus.ideaconsult.net/content/repositories/releases</url> </repository> </repositories> 2) To import a snapshot (e.g.: 4.0.0-SNAPSHOT),...

  • Yannick Djoumbou Yannick Djoumbou posted a comment on ticket #112

    Hi Nina, I have tried quite a few things. I still cant download the .jar files through Maven. I even ceated a dummy project from scratch, without eclipse, and creatig a pacake just fails. Attached is an image with the pom file and the outou from my terminal. Of all the libraries I am importing from my various Maven projects, AMBIT (smarts, tautomers, etc.) is the only one that is consistently not found. The only versions that seem to appear on index are 3.0.2 and 3.0.3-SNAPSHOT, no matter what platform(Mac...

  • Yannick Djoumbou Yannick Djoumbou posted a comment on ticket #112

    OK. I will try that. I hope that will help. Thanks, Yannick

  • Yannick Djoumbou Yannick Djoumbou posted a comment on ticket #112

    Thanks Nina, It looks like it might be a problem with system. I installed Ubuntu 18.04 on a new machine. I have tried different versions of Eclipse, dowloaded index. Either I only get partially results when looking for ambit libraries, or none. It is kind of frustrating.

  • Yannick Djoumbou Yannick Djoumbou posted a comment on ticket #112

    Hi Nina, Thank you so much for the quick reply. I will let you know how that worked out. usually, when including AMBIT, and building the workspace, modbcum is installed automatically. I assume the latest version of AMBT wil automatically install version 1.0.10. Which version of CDK is the current AMBIT version dependent of?

  • Yannick Djoumbou Yannick Djoumbou posted a comment on ticket #113

    Hi Nikolay, Thank you for your quick reply. Best, Yannick

  • Yannick Djoumbou Yannick Djoumbou created ticket #113

    IUPACNAmeGenerator java.lang.NullPointerException issue

  • Yannick Djoumbou Yannick Djoumbou created ticket #112

    net.idea.modbcum issues

  • Yannick Djoumbou Yannick Djoumbou posted a comment on discussion Developers

    Hi all, Is there a function or way to compute the LogD or pKa using the AMBIT library? Thanks, Yannick

  • Yannick Djoumbou Yannick Djoumbou posted a comment on ticket #111

    Hi Nick, How are you doing? Have you had time to look at my previous email from June 16th? I provided you with some of the results I found. It seems there are issues when we first add explicit hydrogens before transforming the molecule. Please could anyone help me out here? Thanks, Yannick

  • Yannick Djoumbou Yannick Djoumbou posted a comment on ticket #111

    Hi all, I actually did some more digging, and realized that because my molecule preprocessing function adds explicit hydrogens, this causes AMBIT to return transforms without seterochemistry.Here are two scenarios: I create a molecule mol and a SMIRKS reaction sr that can transform mol. SMIRKSManager smrkMan = new SMIRKSManager(SilentChemObjectBuilder.getInstance()); IAtomContainer mol = em.smiParser.parseSmiles("OC[C@H]1OC(OC2=CC(OS([O-])(=O)=O)=C([N-][N+]#N)C(OP([O-])([O-])=O)=C2)C@HC@@H[C@@H]1O");...

  • Yannick Djoumbou Yannick Djoumbou created ticket #111

    Problems when applying transformations using stereochemistry

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